Re: [gmx-users] PDB file that can be read in Gromacs
As Justin has pointed out , this process is well documented and UNL is not often found in molecules. No matter what - you will have to do some leg work. Because I run into this almost daily, this may at least get you started. First try using x2top with a selected force field. If your molecule is not too strange, there is a good chance the force field will recognize it. If not, then modify or generate the n2t file ( found in the ff folder ) and again, if the molecule is ‘normal’ only a few atom types may need to be made. Then convert the top file to itp if you wish. If you can use gromos54a7 ff then try using ATB to generate an itp ( which may not be a full QM file ) good luck Paul > On Mar 14, 2019, at 2:27 PM, Justin Lemkul wrote: > > > > On 3/14/19 3:21 PM, Phuong Chau wrote: >> Hello everyone, >> >> I want to generate gromacs topology of a substance (a single chemical) >> which has a pdb file generated by RDKIT from SMILES representation of that >> substance (MolToPDBFile). However, when I input the pdb file generated by >> RDKit, it showed the error of "Residue 'UNL' not found in residue topology >> database". >> >> The general idea is: >> Input: Name of a substance (single chemical) >> Output: pdb file of the substance (does not have to be generated by RDKit) >> and the topology file of its susbtance that is generated by Gromacs. >> >> Could anyone tell me any possible solution to solve this problem? > > pdb2gmx isn't magic :) > > http://manual.gromacs.org/current/user-guide/run-time-errors.html#residue-xxx-not-found-in-residue-topology-database > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > == > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] PDB file that can be read in Gromacs
Hi. First request, try to go through gromacs documentation and tutorials. You will get the clue. Topology of any nonprotein should be generated by a third party software or scripts depending on the forcefield. Have a detailed look into the tutorials. That will definitely help you. Thank you On Fri 15 Mar, 2019, 12:56 AM Phuong Chau, wrote: > Hello everyone, > > I want to generate gromacs topology of a substance (a single chemical) > which has a pdb file generated by RDKIT from SMILES representation of that > substance (MolToPDBFile). However, when I input the pdb file generated by > RDKit, it showed the error of "Residue 'UNL' not found in residue topology > database". > > The general idea is: > Input: Name of a substance (single chemical) > Output: pdb file of the substance (does not have to be generated by RDKit) > and the topology file of its susbtance that is generated by Gromacs. > > Could anyone tell me any possible solution to solve this problem? > > I am new to GROMACS. > > Thank you so much for your help. > Phuong Chau > Smith College '20 > Engineering and Data Science Major > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] PDB file that can be read in Gromacs
On 3/14/19 3:21 PM, Phuong Chau wrote: Hello everyone, I want to generate gromacs topology of a substance (a single chemical) which has a pdb file generated by RDKIT from SMILES representation of that substance (MolToPDBFile). However, when I input the pdb file generated by RDKit, it showed the error of "Residue 'UNL' not found in residue topology database". The general idea is: Input: Name of a substance (single chemical) Output: pdb file of the substance (does not have to be generated by RDKit) and the topology file of its susbtance that is generated by Gromacs. Could anyone tell me any possible solution to solve this problem? pdb2gmx isn't magic :) http://manual.gromacs.org/current/user-guide/run-time-errors.html#residue-xxx-not-found-in-residue-topology-database -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] PDB file that can be read in Gromacs
Hello everyone, I want to generate gromacs topology of a substance (a single chemical) which has a pdb file generated by RDKIT from SMILES representation of that substance (MolToPDBFile). However, when I input the pdb file generated by RDKit, it showed the error of "Residue 'UNL' not found in residue topology database". The general idea is: Input: Name of a substance (single chemical) Output: pdb file of the substance (does not have to be generated by RDKit) and the topology file of its susbtance that is generated by Gromacs. Could anyone tell me any possible solution to solve this problem? I am new to GROMACS. Thank you so much for your help. Phuong Chau Smith College '20 Engineering and Data Science Major -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] PDB file
On 8/15/16 9:30 AM, f.namazi...@sci.ui.ac.ir wrote: Hi Dear all; What are these columns "1.00" and "0.00" in PDB file? Google knows all about PDB format. -Justin for example: ATOM 10 N LEU A 2 4.595 6.365 3.756 1.00 0.00 N ATOM 11 CA LEU A 2 4.471 5.443 2.633 1.00 0.00 C ATOM 12 C LEU A 2 5.841 5.176 2.015 1.00 0.00 C ATOM 13 O LEU A 2 6.205 4.029 1.755 1.00 0.00 O ATOM 14 CB LEU A 2 3.526 6.037 1.578 1.00 0.00 C ATOM 15 CG LEU A 2 2.790 4.919 0.823 1.00 0.00 C ATOM 16 CD1 LEU A 2 3.803 3.916 0.262 1.00 0.00 C ATOM 17 CD2 LEU A 2 1.817 4.196 1.769 1.00 0.00 C ATOM 18 H LEU A 2 4.169 7.246 3.704 1.00 0.00 H ATOM 19 HA LEU A 2 4.063 4.514 2.992 1.00 0.00 H ATOM 20 HB2 LEU A 2 2.804 6.675 2.065 1.00 0.00 H ATOM 21 HB3 LEU A 2 4.099 6.623 0.873 1.00 0.00 H ATOM 22 HG LEU A 2 2.234 5.353 0.004 1.00 0.00 H ATOM 23 HD11 LEU A 2 4.648 4.447 -0.148 1.00 0.00 H ATOM 24 HD12 LEU A 2 3.334 3.331 -0.516 1.00 0.00 H ATOM 25 HD13 LEU A 2 4.137 3.260 1.052 1.00 0.00 H ATOM 26 HD21 LEU A 2 0.941 3.892 1.216 1.00 0.00 H ATOM 27 HD22 LEU A 2 1.522 4.860 2.568 1.00 0.00 H ATOM 28 HD23 LEU A 2 2.296 3.323 2.188 1.00 0.00 H The Best. Farzaneh. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] PDB file
Hi Dear all; What are these columns "1.00" and "0.00" in PDB file? for example: ATOM 10 N LEU A 2 4.595 6.365 3.756 1.00 0.00 N ATOM 11 CA LEU A 2 4.471 5.443 2.633 1.00 0.00 C ATOM 12 C LEU A 2 5.841 5.176 2.015 1.00 0.00 C ATOM 13 O LEU A 2 6.205 4.029 1.755 1.00 0.00 O ATOM 14 CB LEU A 2 3.526 6.037 1.578 1.00 0.00 C ATOM 15 CG LEU A 2 2.790 4.919 0.823 1.00 0.00 C ATOM 16 CD1 LEU A 2 3.803 3.916 0.262 1.00 0.00 C ATOM 17 CD2 LEU A 2 1.817 4.196 1.769 1.00 0.00 C ATOM 18 H LEU A 2 4.169 7.246 3.704 1.00 0.00 H ATOM 19 HA LEU A 2 4.063 4.514 2.992 1.00 0.00 H ATOM 20 HB2 LEU A 2 2.804 6.675 2.065 1.00 0.00 H ATOM 21 HB3 LEU A 2 4.099 6.623 0.873 1.00 0.00 H ATOM 22 HG LEU A 2 2.234 5.353 0.004 1.00 0.00 H ATOM 23 HD11 LEU A 2 4.648 4.447 -0.148 1.00 0.00 H ATOM 24 HD12 LEU A 2 3.334 3.331 -0.516 1.00 0.00 H ATOM 25 HD13 LEU A 2 4.137 3.260 1.052 1.00 0.00 H ATOM 26 HD21 LEU A 2 0.941 3.892 1.216 1.00 0.00 H ATOM 27 HD22 LEU A 2 1.522 4.860 2.568 1.00 0.00 H ATOM 28 HD23 LEU A 2 2.296 3.323 2.188 1.00 0.00 H The Best. Farzaneh. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] *.pdb file for the Tip4p/ice model
Thanks for a good idea. I am also doing the same. Sheelan S C Phys Chem Div From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Elton Carvalho [elto...@gmail.com] Sent: Monday, April 04, 2016 8:37 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] *.pdb file for the Tip4p/ice model Since ice is a crystal, you can build a crystalline unit cell by hand (the unit cell will have one or two water molecules, so it's pretty easy to do it by hand, you just have to be careful to use the same atom ordering as the topology) and replicate it using gmx genconf so the crystal has the dimensions you need. On Thu, Mar 31, 2016 at 1:32 AM, Sheelan Sengupta wrote: > will put an ice nuclei (small ice crystal) in a box of water to study the ice > nucleation. water and ice will be modeled by tip4p. > > Sheelan S C > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Christopher > Neale [chris.ne...@alum.utoronto.ca] > Sent: Wednesday, March 30, 2016 11:25 PM > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] *.pdb file for the Tip4p/ice model > > Need it for what? To solvate a solute with genbox or for some other sytem > setup needs? Common protocol would be to simply use tip4p.gro and then to > equilibrate it with the new tip4p/ice parameters. tip4p.gro is in > share/gromacs/top/ > > Chris. > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > on behalf of Sheelan > Sengupta > Sent: 30 March 2016 05:45 > To: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: [gmx-users] *.pdb file for the Tip4p/ice model > > need the *.pdb file of Tip4p/ice model. Please help. > > Regards, > Sheelan S C > Phys Chem Div > > > > Disclaimer: > > This message and the information contained herein is proprietary and > confidential and subject to the policy statement of the National Chemical > Laboratory, Pune, India. You may review the policy at > http://www.ncl-india.org/files/TermsAndConditions/WebmailDisclamer.aspx > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. > > > > Disclaimer: > > This message and the information contained herein is proprietary and > confidential and subject to the policy statement of the National Chemical > Laboratory, Pune, India. You may review the policy at > http://www.ncl-india.org/files/TermsAndConditions/WebmailDisclamer.aspx > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Elton Carvalho -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. Disclaimer: This message and the information contained herein is proprietary and confidential and subject to the policy statement of the National Chemical Laboratory, Pune, India. You may review the policy at http://www.ncl-india.org/files/TermsAndConditions/WebmailDisclamer.aspx -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] *.pdb file for the Tip4p/ice model
Since ice is a crystal, you can build a crystalline unit cell by hand (the unit cell will have one or two water molecules, so it's pretty easy to do it by hand, you just have to be careful to use the same atom ordering as the topology) and replicate it using gmx genconf so the crystal has the dimensions you need. On Thu, Mar 31, 2016 at 1:32 AM, Sheelan Sengupta wrote: > will put an ice nuclei (small ice crystal) in a box of water to study the ice > nucleation. water and ice will be modeled by tip4p. > > Sheelan S C > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Christopher > Neale [chris.ne...@alum.utoronto.ca] > Sent: Wednesday, March 30, 2016 11:25 PM > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] *.pdb file for the Tip4p/ice model > > Need it for what? To solvate a solute with genbox or for some other sytem > setup needs? Common protocol would be to simply use tip4p.gro and then to > equilibrate it with the new tip4p/ice parameters. tip4p.gro is in > share/gromacs/top/ > > Chris. > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > on behalf of Sheelan > Sengupta > Sent: 30 March 2016 05:45 > To: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: [gmx-users] *.pdb file for the Tip4p/ice model > > need the *.pdb file of Tip4p/ice model. Please help. > > Regards, > Sheelan S C > Phys Chem Div > > > > Disclaimer: > > This message and the information contained herein is proprietary and > confidential and subject to the policy statement of the National Chemical > Laboratory, Pune, India. You may review the policy at > http://www.ncl-india.org/files/TermsAndConditions/WebmailDisclamer.aspx > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. > > > > Disclaimer: > > This message and the information contained herein is proprietary and > confidential and subject to the policy statement of the National Chemical > Laboratory, Pune, India. You may review the policy at > http://www.ncl-india.org/files/TermsAndConditions/WebmailDisclamer.aspx > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Elton Carvalho -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] *.pdb file for the Tip4p/ice model
will put an ice nuclei (small ice crystal) in a box of water to study the ice nucleation. water and ice will be modeled by tip4p. Sheelan S C From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Christopher Neale [chris.ne...@alum.utoronto.ca] Sent: Wednesday, March 30, 2016 11:25 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] *.pdb file for the Tip4p/ice model Need it for what? To solvate a solute with genbox or for some other sytem setup needs? Common protocol would be to simply use tip4p.gro and then to equilibrate it with the new tip4p/ice parameters. tip4p.gro is in share/gromacs/top/ Chris. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Sheelan Sengupta Sent: 30 March 2016 05:45 To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] *.pdb file for the Tip4p/ice model need the *.pdb file of Tip4p/ice model. Please help. Regards, Sheelan S C Phys Chem Div Disclaimer: This message and the information contained herein is proprietary and confidential and subject to the policy statement of the National Chemical Laboratory, Pune, India. You may review the policy at http://www.ncl-india.org/files/TermsAndConditions/WebmailDisclamer.aspx -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. Disclaimer: This message and the information contained herein is proprietary and confidential and subject to the policy statement of the National Chemical Laboratory, Pune, India. You may review the policy at http://www.ncl-india.org/files/TermsAndConditions/WebmailDisclamer.aspx -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] *.pdb file for the Tip4p/ice model
Need it for what? To solvate a solute with genbox or for some other sytem setup needs? Common protocol would be to simply use tip4p.gro and then to equilibrate it with the new tip4p/ice parameters. tip4p.gro is in share/gromacs/top/ Chris. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Sheelan Sengupta Sent: 30 March 2016 05:45 To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] *.pdb file for the Tip4p/ice model need the *.pdb file of Tip4p/ice model. Please help. Regards, Sheelan S C Phys Chem Div Disclaimer: This message and the information contained herein is proprietary and confidential and subject to the policy statement of the National Chemical Laboratory, Pune, India. You may review the policy at http://www.ncl-india.org/files/TermsAndConditions/WebmailDisclamer.aspx -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] *.pdb file for the Tip4p/ice model
need the *.pdb file of Tip4p/ice model. Please help. Regards, Sheelan S C Phys Chem Div Disclaimer: This message and the information contained herein is proprietary and confidential and subject to the policy statement of the National Chemical Laboratory, Pune, India. You may review the policy at http://www.ncl-india.org/files/TermsAndConditions/WebmailDisclamer.aspx -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Pdb file
Exactly. Gaseous LJ systems above a certain density will have a positive PE. Mark On Wed, Aug 12, 2015 at 9:23 PM sujithkakkat . wrote: > Hello, > > I guess it is not unusual for gaseous systems to have positive energy. I > hope that the Fmax criteria is satisfied. > > Sujith. > > On Wed, Aug 12, 2015 at 10:30 AM, Sunil Ghimire > wrote: > > > I mean potential energy of system (1600 argon atoms) is positive after > > energy mininization . > > On 12 Aug 2015 16:58, "Vitaly V. Chaban" wrote: > > > > > L_BFGS > > > > > > > > > > > > > > > On Tue, Aug 11, 2015 at 11:37 PM, Sunil Ghimire > > > wrote: > > > > I created the pdb file by genconf but the system was not minimized, i > > got > > > > positive potential energy. What may be the problem? > > > > On 11 Aug 2015 19:38, "Mark Abraham" > wrote: > > > > > > > >> Hi, > > > >> > > > >> gmx genconf on a small box with a single argon is a useful starting > > > point. > > > >> > > > >> Mark > > > >> > > > >> On Tue, Aug 11, 2015 at 3:16 PM Sunil Ghimire < > > ghimiresuni...@gmail.com > > > > > > > >> wrote: > > > >> > > > >> > How can i create the .pdb file for 1600 atoms of argon ? > > > >> > -- > > > >> > Gromacs Users mailing list > > > >> > > > > >> > * Please search the archive at > > > >> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List > before > > > >> > posting! > > > >> > > > > >> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > >> > > > > >> > * For (un)subscribe requests visit > > > >> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > > or > > > >> > send a mail to gmx-users-requ...@gromacs.org. > > > >> > > > > >> -- > > > >> Gromacs Users mailing list > > > >> > > > >> * Please search the archive at > > > >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > >> posting! > > > >> > > > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > >> > > > >> * For (un)subscribe requests visit > > > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or > > > >> send a mail to gmx-users-requ...@gromacs.org. > > > >> > > > > -- > > > > Gromacs Users mailing list > > > > > > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > posting! > > > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > * For (un)subscribe requests visit > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or > > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > posting! > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > * For (un)subscribe requests visit > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Pdb file
Hello, I guess it is not unusual for gaseous systems to have positive energy. I hope that the Fmax criteria is satisfied. Sujith. On Wed, Aug 12, 2015 at 10:30 AM, Sunil Ghimire wrote: > I mean potential energy of system (1600 argon atoms) is positive after > energy mininization . > On 12 Aug 2015 16:58, "Vitaly V. Chaban" wrote: > > > L_BFGS > > > > > > > > > > On Tue, Aug 11, 2015 at 11:37 PM, Sunil Ghimire > > wrote: > > > I created the pdb file by genconf but the system was not minimized, i > got > > > positive potential energy. What may be the problem? > > > On 11 Aug 2015 19:38, "Mark Abraham" wrote: > > > > > >> Hi, > > >> > > >> gmx genconf on a small box with a single argon is a useful starting > > point. > > >> > > >> Mark > > >> > > >> On Tue, Aug 11, 2015 at 3:16 PM Sunil Ghimire < > ghimiresuni...@gmail.com > > > > > >> wrote: > > >> > > >> > How can i create the .pdb file for 1600 atoms of argon ? > > >> > -- > > >> > Gromacs Users mailing list > > >> > > > >> > * Please search the archive at > > >> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > >> > posting! > > >> > > > >> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > >> > > > >> > * For (un)subscribe requests visit > > >> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or > > >> > send a mail to gmx-users-requ...@gromacs.org. > > >> > > > >> -- > > >> Gromacs Users mailing list > > >> > > >> * Please search the archive at > > >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > >> posting! > > >> > > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > >> > > >> * For (un)subscribe requests visit > > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > >> send a mail to gmx-users-requ...@gromacs.org. > > >> > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > * For (un)subscribe requests visit > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Pdb file
I mean potential energy of system (1600 argon atoms) is positive after energy mininization . On 12 Aug 2015 16:58, "Vitaly V. Chaban" wrote: > L_BFGS > > > > > On Tue, Aug 11, 2015 at 11:37 PM, Sunil Ghimire > wrote: > > I created the pdb file by genconf but the system was not minimized, i got > > positive potential energy. What may be the problem? > > On 11 Aug 2015 19:38, "Mark Abraham" wrote: > > > >> Hi, > >> > >> gmx genconf on a small box with a single argon is a useful starting > point. > >> > >> Mark > >> > >> On Tue, Aug 11, 2015 at 3:16 PM Sunil Ghimire > > >> wrote: > >> > >> > How can i create the .pdb file for 1600 atoms of argon ? > >> > -- > >> > Gromacs Users mailing list > >> > > >> > * Please search the archive at > >> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >> > posting! > >> > > >> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > > >> > * For (un)subscribe requests visit > >> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >> > send a mail to gmx-users-requ...@gromacs.org. > >> > > >> -- > >> Gromacs Users mailing list > >> > >> * Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >> posting! > >> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > >> * For (un)subscribe requests visit > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >> send a mail to gmx-users-requ...@gromacs.org. > >> > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] pdb file for united atom force fields
On 8/12/15 12:46 AM, faride badalkhani wrote: Dear Gromacs users, I need to work with a united atom FF, but I have defined all the Hydrogens in my pdb file. Does it cause any problem in MD procedure? Well, the UA force field won't use (most of) the H, so they obviously need to be removed. If this is a biomolecule, pdb2gmx -ignh takes care of this for you. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Pdb file
L_BFGS On Tue, Aug 11, 2015 at 11:37 PM, Sunil Ghimire wrote: > I created the pdb file by genconf but the system was not minimized, i got > positive potential energy. What may be the problem? > On 11 Aug 2015 19:38, "Mark Abraham" wrote: > >> Hi, >> >> gmx genconf on a small box with a single argon is a useful starting point. >> >> Mark >> >> On Tue, Aug 11, 2015 at 3:16 PM Sunil Ghimire >> wrote: >> >> > How can i create the .pdb file for 1600 atoms of argon ? >> > -- >> > Gromacs Users mailing list >> > >> > * Please search the archive at >> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> > posting! >> > >> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > >> > * For (un)subscribe requests visit >> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> > send a mail to gmx-users-requ...@gromacs.org. >> > >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-requ...@gromacs.org. >> > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Pdb file
Hi, When can a single argon-argon interaction have a negative potential energy? Mark On Wed, Aug 12, 2015 at 4:37 AM Sunil Ghimire wrote: > I created the pdb file by genconf but the system was not minimized, i got > positive potential energy. What may be the problem? > On 11 Aug 2015 19:38, "Mark Abraham" wrote: > > > Hi, > > > > gmx genconf on a small box with a single argon is a useful starting > point. > > > > Mark > > > > On Tue, Aug 11, 2015 at 3:16 PM Sunil Ghimire > > wrote: > > > > > How can i create the .pdb file for 1600 atoms of argon ? > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > posting! > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > * For (un)subscribe requests visit > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] pdb file for united atom force fields
Dear Gromacs users, I need to work with a united atom FF, but I have defined all the Hydrogens in my pdb file. Does it cause any problem in MD procedure? Truly yours, Farideh -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Pdb file
I created the pdb file by genconf but the system was not minimized, i got positive potential energy. What may be the problem? On 11 Aug 2015 19:38, "Mark Abraham" wrote: > Hi, > > gmx genconf on a small box with a single argon is a useful starting point. > > Mark > > On Tue, Aug 11, 2015 at 3:16 PM Sunil Ghimire > wrote: > > > How can i create the .pdb file for 1600 atoms of argon ? > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Pdb file
Hi, gmx genconf on a small box with a single argon is a useful starting point. Mark On Tue, Aug 11, 2015 at 3:16 PM Sunil Ghimire wrote: > How can i create the .pdb file for 1600 atoms of argon ? > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Pdb file
How can i create the .pdb file for 1600 atoms of argon ? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
